Skim has a "Take Snapshot" feature which allows you to print anything which is visually on the page. It also has a "Convert Notes" feature which turns PDF annotations into "skim notes" which you can then manipulate.

thank you. The "convert notes" feature lets me convert the notes to "real" skim notes, however to those which are displayed also only as a symbol on the page, so the real content of the notes is not displayed on the page and I still don't see how to print it (I also tried the snapshot feature). :-(
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MartinMay 7 '11 at 2:47

Weird, because when I used the snapshot feature I got a pdf with notes on page if they were skim notes, I can see the garish yellow boxes everywhere. As it is supposed to print out essentially a screenshot of the content(and you can see the notes in the screenshot)
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hobsMay 7 '11 at 12:40

I think it depends on the kind of note: The notes were automatically converted to an anchored Skim note which is represented in the document only by a symbol and is displayed in a separate window
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MartinMay 8 '11 at 14:22

There is a really simple yet robust tool for extracting highlights, notes and images from your pdf-files available at: http://www.sumnotes.net . Not only it supports various advanced features like exporting to DOC and TXT formats, but it also allows you to send extracted highlights into your Evernote account or email. All desktop browsers and operating systems are supported. We are in cloud, so no installation is needed. Try it out.

I faced the same problem. To resolve it I created a free service to extract annotations from PDF to CSV: http://exportpdf.info . It exports only sticky and text notes, it does not export highlights and images. You can edit/print CSV files with any major editor like Microsoft Excel or LibreOffice Calc.